Calcium in PDB 7ln7: X-Ray Radiation Damage Series on Proteinase K at 277K, Crystal Structure, Dataset 1

All present enzymatic activity of X-Ray Radiation Damage Series on Proteinase K at 277K, Crystal Structure, Dataset 1:
3.4.21.64;

The structure of X-Ray Radiation Damage Series on Proteinase K at 277K, Crystal Structure, Dataset 1, PDB code: 7ln7 was solved by F.Yabukarski, T.Doukov, D.Herschlag, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.91 / 1.02
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	67.82, 67.82, 101.865, 90, 90, 90
R / Rfree (%)	12.3 / 13.8

The binding sites of Calcium atom in the X-Ray Radiation Damage Series on Proteinase K at 277K, Crystal Structure, Dataset 1 (pdb code 7ln7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the X-Ray Radiation Damage Series on Proteinase K at 277K, Crystal Structure, Dataset 1, PDB code: 7ln7:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the X-Ray Radiation Damage Series on Proteinase K at 277K, Crystal Structure, Dataset 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of X-Ray Radiation Damage Series on Proteinase K at 277K, Crystal Structure, Dataset 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:7.6 occ:0.40 CA A:CA304 0.0 7.6 0.4 CA A:CA304 2.1 26.1 0.6 O A:HOH434 2.4 20.7 1.0 O A:HOH540 2.4 11.8 1.0 OD2 A:ASP200 2.4 8.4 1.0 O A:VAL177 2.4 8.6 1.0 O A:PRO175 2.5 10.6 1.0 O A:HOH619 2.6 24.3 1.0 OD1 A:ASP200 2.7 12.8 1.0 CG A:ASP200 2.9 8.9 1.0 C A:PRO175 3.5 9.1 1.0 C A:VAL177 3.7 7.1 1.0 HA A:CYS178 3.7 7.5 1.0 HA A:PRO175 3.7 11.6 1.0 H A:THR179 3.9 7.0 1.0 H A:VAL177 4.2 9.6 1.0 O A:VAL198 4.2 10.4 0.3 CA A:PRO175 4.2 9.7 1.0 N A:VAL177 4.2 8.0 1.0 CB A:ASP200 4.4 8.0 1.0 O A:VAL198 4.4 8.8 0.7 O A:HOH660 4.4 32.3 1.0 O A:GLU174 4.4 8.5 1.0 HA A:SER176 4.5 10.0 1.0 CA A:CYS178 4.5 6.3 1.0 N A:SER176 4.5 8.6 1.0 C A:SER176 4.5 8.1 1.0 N A:CYS178 4.5 6.4 1.0 O A:HOH531 4.6 31.5 1.0 CA A:VAL177 4.6 7.3 1.0 N A:THR179 4.7 5.9 1.0 HB2 A:ASP200 4.7 9.6 1.0 O A:HOH508 4.7 17.9 0.8 O A:HOH680 4.7 42.4 1.0 HB3 A:ASP200 4.7 9.6 1.0 CA A:SER176 4.8 8.3 1.0 HG22 A:VAL198 4.9 15.7 0.7 HG23 A:VAL198 4.9 15.7 0.7 OG1 A:THR179 4.9 7.8 1.0 SG A:CYS249 4.9 8.8 1.0 HB A:THR179 4.9 8.1 1.0

Calcium binding site 2 out of 2 in the X-Ray Radiation Damage Series on Proteinase K at 277K, Crystal Structure, Dataset 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of X-Ray Radiation Damage Series on Proteinase K at 277K, Crystal Structure, Dataset 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:26.1 occ:0.60 CA A:CA304 0.0 26.1 0.6 CA A:CA304 2.1 7.6 0.4 O A:HOH619 2.7 24.3 1.0 O A:VAL177 2.8 8.6 1.0 O A:HOH660 2.9 32.3 1.0 O A:HOH508 3.0 17.9 0.8 O A:PRO175 3.1 10.6 1.0 OD1 A:ASP200 3.2 12.8 1.0 OD2 A:ASP200 3.6 8.4 1.0 CG A:ASP200 3.6 8.9 1.0 O A:HOH656 3.6 45.9 1.0 C A:VAL177 3.7 7.1 1.0 HA A:CYS178 3.8 7.5 1.0 SG A:CYS249 3.9 8.8 1.0 HA A:SER176 4.0 10.0 1.0 HB3 A:CYS249 4.0 10.6 1.0 C A:SER176 4.0 8.1 1.0 O A:SER176 4.1 10.2 1.0 O A:HOH434 4.2 20.7 1.0 N A:VAL177 4.2 8.0 1.0 C A:PRO175 4.3 9.1 1.0 O A:HOH540 4.3 11.8 1.0 CA A:SER176 4.5 8.3 1.0 N A:CYS178 4.5 6.4 1.0 CB A:CYS249 4.5 8.8 1.0 CA A:VAL177 4.5 7.3 1.0 CA A:CYS178 4.5 6.3 1.0 H A:VAL177 4.6 9.6 1.0 HA A:VAL177 4.7 8.8 1.0 O A:HOH553 4.7 14.1 0.4 O A:HOH663 4.7 38.4 1.0 HB2 A:CYS249 4.7 10.6 1.0 HB3 A:ASP200 4.8 9.6 1.0 CB A:ASP200 4.8 8.0 1.0 N A:SER176 4.8 8.6 1.0 O A:HOH492 4.8 27.3 1.0 H A:THR179 5.0 7.0 1.0

F.Yabukarski, T.Doukov, D.A.Mokhtari, S.Du, D.Herschlag. Evaluating the Impact of X-Ray Damage on Conformational Heterogeneity in Room-Temperature (277 K) and Cryo-Cooled Protein Crystals. Acta Crystallogr D Struct V. 78 945 2022BIOL.
ISSN: ISSN 2059-7983
PubMed: 35916220
DOI: 10.1107/S2059798322005939